[gmx-users] Pulling

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Mar 16 10:45:17 CET 2011

Dear Chris
Thanks for your reply

2-When you limit your sampling phase space,it can make some Errors,Because
you may ignore
some important regions(where you don't know them and you can't predict
In the other hands,When we pull drug along a line,although we had not
restrain it, but in fact they are equivalent!
Because the orientation of drug dosen't change during the simulation(Because
doing umberella sampling dosen't change the orientation too).
Is it possible to do Umbrella Sampling while the drug be free to rotate
along with oscilation in windows?

On Tue, Mar 15, 2011 at 9:49 AM, <chris.neale at utoronto.ca> wrote:

> 1. yes. it is acceptable. It is different, but neither method is de facto
> better.
> 2. to enhance convergence by limiting the amount of phase space that must
> be sampled. Changing the restraints can change the profile, but if you care
> only about the integrated standard binding free energy then it does not
> change the converged result. See, for example, D. L. Mobley, J. D. Chodera,
> K. A. Dill. "On the use of orientational restraints and symmetry number
> corrections in alchemical free energy calculations", ...
> Chris.
> -- original message --
> Dear All
> Afew question about Pulling in Umberella Sampling
> 1-the goal of pulling is making some primary structures (in different
> distances) to do umberella sampling for each one of them.
>  I can make these states by transporting my ligands along a vector to
> prepare these primary structures.Is this correct?Now I can do US for each
> one!without any need to doing pulling.
> 2-Why do we keep fix the relative orientation of Protein-ligand during the
> pulling ? I think changing the orientation of ligand during the
> pulling(suppose the protein is restrain) can chang our result?
>  Because our umbrella sampling maintain this orientation too.am I right?
> Thanks in advance
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